Job ID = 6367403 SRX = SRX331162 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:28:36 prefetch.2.10.7: 1) Downloading 'SRR947394'... 2020-06-15T23:28:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:29:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:29:16 prefetch.2.10.7: 'SRR947394' is valid 2020-06-15T23:29:16 prefetch.2.10.7: 1) 'SRR947394' was downloaded successfully Read 3940365 spots for SRR947394/SRR947394.sra Written 3940365 spots for SRR947394/SRR947394.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:35 3940365 reads; of these: 3940365 (100.00%) were unpaired; of these: 1083196 (27.49%) aligned 0 times 2376684 (60.32%) aligned exactly 1 time 480485 (12.19%) aligned >1 times 72.51% overall alignment rate Time searching: 00:00:35 Overall time: 00:00:35 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 499124 / 2857169 = 0.1747 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:31:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:31:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:09: 1000000 INFO @ Tue, 16 Jun 2020 08:31:15: 2000000 INFO @ Tue, 16 Jun 2020 08:31:17: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:17: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:17: #1 total tags in treatment: 2358045 INFO @ Tue, 16 Jun 2020 08:31:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:31:17: #1 tags after filtering in treatment: 2358045 INFO @ Tue, 16 Jun 2020 08:31:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:17: #2 number of paired peaks: 1045 INFO @ Tue, 16 Jun 2020 08:31:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:17: #2 predicted fragment length is 161 bps INFO @ Tue, 16 Jun 2020 08:31:17: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 16 Jun 2020 08:31:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.05_model.r INFO @ Tue, 16 Jun 2020 08:31:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:31:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.05_summits.bed INFO @ Tue, 16 Jun 2020 08:31:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1746 records, 4 fields): 3 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:31:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:31:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:39: 1000000 INFO @ Tue, 16 Jun 2020 08:31:45: 2000000 INFO @ Tue, 16 Jun 2020 08:31:47: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:47: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:47: #1 total tags in treatment: 2358045 INFO @ Tue, 16 Jun 2020 08:31:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:31:47: #1 tags after filtering in treatment: 2358045 INFO @ Tue, 16 Jun 2020 08:31:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:47: #2 number of paired peaks: 1045 INFO @ Tue, 16 Jun 2020 08:31:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:47: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:47: #2 predicted fragment length is 161 bps INFO @ Tue, 16 Jun 2020 08:31:47: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 16 Jun 2020 08:31:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.10_model.r INFO @ Tue, 16 Jun 2020 08:31:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:31:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.10_summits.bed INFO @ Tue, 16 Jun 2020 08:31:55: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (916 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:32:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:32:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:09: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:32:13: 2000000 INFO @ Tue, 16 Jun 2020 08:32:15: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:32:15: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:32:15: #1 total tags in treatment: 2358045 INFO @ Tue, 16 Jun 2020 08:32:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:32:15: #1 tags after filtering in treatment: 2358045 INFO @ Tue, 16 Jun 2020 08:32:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:15: #2 number of paired peaks: 1045 INFO @ Tue, 16 Jun 2020 08:32:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:15: #2 predicted fragment length is 161 bps INFO @ Tue, 16 Jun 2020 08:32:15: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 16 Jun 2020 08:32:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.20_model.r INFO @ Tue, 16 Jun 2020 08:32:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:32:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331162/SRX331162.20_summits.bed INFO @ Tue, 16 Jun 2020 08:32:24: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (484 records, 4 fields): 2 millis CompletedMACS2peakCalling